AiPD: Autoinhibited Protein Database

Q13907

Gene name	IDI1
Protein name	Isopentenyl-diphosphate Delta-isomerase 1
Names	Isopentenyl pyrophosphate isomerase 1, IPP isomerase 1, IPPI1
Species	Homo sapiens (Human)
KEGG Pathway	hsa:3422
EC number	5.3.3.2: Transposing C=C bonds
Protein Class

Descriptions

The autoinhibited protein was predicted that may have potential autoinhibitory elements via cis-regPred.

Autoinhibitory domains (AIDs)

58-135 (Predicted disordered autoinhibitory region) PR

Target domain
Relief mechanism
Assay	cis-regPred

AID

58-135 (Predicted disordered autoinhibitory region)

Target domain

Relief mechanism

Assay

cis-regPred

Accessory elements

No accessory elements

References

Yeon JH et al. (2016) "Systems-wide Identification of cis-Regulatory Elements in Proteins", Cell Systems, 2, 89-100

Autoinhibited structure

Activated structure

5 structures for Q13907

Entry ID	Method	Resolution	Chain	Position	Source
2DHO	X-ray	160 A	A	1-227	PDB
2I6K	X-ray	200 A	A/B	1-227	PDB
2ICJ	X-ray	170 A	A	1-227	PDB
2ICK	X-ray	193 A	A	1-227	PDB
AF-Q13907-F1	Predicted				AlphaFoldDB

141 variants for Q13907

Variant ID(s)	Position	Change	Description	Diseaes Association	Provenance
CA5383747 rs754551250	2	P>S		No	ClinGen ExAC gnomAD
rs766088534 CA5383745	4	I>V		No	ClinGen ExAC gnomAD
rs767934669 CA5383742	10	D>N		No	ClinGen ExAC TOPMed gnomAD
CA5383740 rs373579438	13	Q>R		No	ClinGen ESP ExAC TOPMed gnomAD
rs1048256396 CA201212916	14	V>F		No	ClinGen gnomAD
CA375853628 rs1048256396	14	V>L		No	ClinGen gnomAD
rs574248854 CA201212915	18	A>G		No	ClinGen gnomAD
CA375853601 rs574248854	18	A>V		No	ClinGen gnomAD
rs775521932 CA5383736	20	M>L		No	ClinGen ExAC TOPMed gnomAD
rs186649780 CA5383735	21	C>R		No	ClinGen 1000Genomes ExAC TOPMed gnomAD
CA375853569 rs1479426324	23	L>V		No	ClinGen gnomAD
rs746121163 CA5383734	26	E>*		No	ClinGen ExAC gnomAD
CA5383733 rs777622677	28	D>Y	Variant assessed as Somatic; 4.62e-05 impact. [NCI-TCGA]	No	ClinGen ExAC NCI-TCGA gnomAD
CA5383732 rs758328751	31	I>T		No	ClinGen ExAC gnomAD
CA375853510 rs1470218707	31	I>V		No	ClinGen TOPMed
CA201212913 rs889377532	33	A>S		No	ClinGen TOPMed gnomAD
CA375853499 rs889377532	33	A>T		No	ClinGen TOPMed gnomAD
rs1387781836 CA375853481	35	T>I		No	ClinGen TOPMed
rs1305960783 CA375853479	36	K>E		No	ClinGen gnomAD
rs11556792 CA201212912	38	N>I		No	ClinGen Ensembl
rs931193312 CA201212911	39	C>Y		No	ClinGen gnomAD
CA5383730 rs748042759	41	L>P		No	ClinGen ExAC gnomAD
CA5383728 rs755747753	43	E>K		No	ClinGen ExAC TOPMed gnomAD
CA201212908 rs898035148	45	I>T		No	ClinGen TOPMed
CA201212909 rs918520734	45	I>V		No	ClinGen TOPMed
CA375853394 rs1454725781	48	G>R		No	ClinGen gnomAD
rs758705449 CA375853358	51	H>L		No	ClinGen ExAC TOPMed gnomAD
rs758705449 CA5383681	51	H>R		No	ClinGen ExAC TOPMed gnomAD
rs1564485084 CA375853362	51	H>Y		No	ClinGen Ensembl
CA5383680 rs753184688	52	R>*		No	ClinGen ExAC gnomAD
rs1233569212 COSM3806420 COSM3806419 CA375853354	52	R>Q	Variant assessed as Somatic; impact. breast [NCI-TCGA, Cosmic]	No	ClinGen cosmic curated NCI-TCGA TOPMed
rs1459169299 CA375853347	53	A>G		No	ClinGen TOPMed
CA201212857 rs11556791	54	F>L		No	ClinGen Ensembl
CA375853330 rs1445126982	56	V>I		No	ClinGen TOPMed gnomAD
CA375853308 rs1164839896	59	F>L		No	ClinGen TOPMed
CA375853288 rs1564485007 COSM914687	61	T>I	Variant assessed as Somatic; 0.0 impact. endometrium [NCI-TCGA, Cosmic]	No	ClinGen cosmic curated Ensembl NCI-TCGA
rs1564485007 CA375853290	61	T>S		No	ClinGen Ensembl
rs1409048808 CA375853284	62	E>G		No	ClinGen TOPMed
rs149253949 CA5383676	62	E>K		No	ClinGen ESP ExAC TOPMed gnomAD
CA201212855 rs922939678	64	K>R		No	ClinGen TOPMed
rs745953610 CA201212854	65	L>F		No	ClinGen gnomAD
rs745953610 CA375853265	65	L>I		No	ClinGen gnomAD
rs1384811111 CA375853248	68	Q>*		No	ClinGen gnomAD
rs766606824 CA201212853	68	Q>H		No	ClinGen ExAC TOPMed gnomAD
rs1476424643 CA375853229	70	R>S		No	ClinGen TOPMed gnomAD
rs1243266082 CA375853222	72	D>N		No	ClinGen gnomAD
CA375853219 rs1564484945	72	D>V		No	ClinGen Ensembl
rs770974282 CA201212851	75	I>M		No	ClinGen ExAC TOPMed gnomAD
CA375853187 rs1214311461	77	F>L		No	ClinGen TOPMed
CA5383665 rs776111278	82	T>M		No	ClinGen ExAC gnomAD
rs748485569 CA5383660	86	C>Y		No	ClinGen ExAC gnomAD
CA201212800 rs78687080	88	H>N		No	ClinGen Ensembl
rs374609861 CA5383658	90	L>I		No	ClinGen ESP ExAC TOPMed gnomAD
rs754453356 CA5383657	92	N>S		No	ClinGen ExAC TOPMed gnomAD
CA5383655 rs766508803	94	A>S		No	ClinGen ExAC gnomAD
CA5383654 rs756264901	95	E>K		No	ClinGen ExAC TOPMed gnomAD
rs147132395 CA5383653	97	E>D		No	ClinGen 1000Genomes ESP ExAC TOPMed gnomAD
CA5383652 rs767653210	99	S>T		No	ClinGen ExAC gnomAD
rs1466221257 CA375853009	101	A>D		No	ClinGen TOPMed
rs775112470 CA5383650	101	A>T		No	ClinGen ExAC gnomAD
CA375853004 rs1333375473	102	L>F		No	ClinGen TOPMed
rs765142925 CA5383649	104	V>M		No	ClinGen ExAC gnomAD
rs1432151791 CA375852987	105	R>K		No	ClinGen gnomAD
CA5383647 rs776566959	106	R>*	Variant assessed as Somatic; 0.0 impact. [NCI-TCGA]	No	ClinGen ExAC NCI-TCGA TOPMed gnomAD
CA375852968 rs955174456	108	A>G		No	ClinGen TOPMed
CA201212797 rs955174456	108	A>V		No	ClinGen TOPMed
rs1481434617 CA375852956	110	R>K		No	ClinGen gnomAD
CA201212796 rs771603096	111	R>P		No	ClinGen ExAC TOPMed gnomAD
CA5383643 rs771603096	111	R>Q		No	ClinGen ExAC TOPMed gnomAD
rs772874055 CA5383644	111	R>W		No	ClinGen ExAC TOPMed gnomAD
rs754274098 CA201212795	112	L>V		No	ClinGen Ensembl
rs747875115 CA5383642	114	A>P		No	ClinGen ExAC TOPMed gnomAD
CA5383639 rs749745448	119	P>S		No	ClinGen ExAC gnomAD
CA375852901 rs776674889	120	L>V		No	ClinGen ExAC TOPMed gnomAD
CA5383636 rs750505686	121	E>D		No	ClinGen ExAC gnomAD
rs1319934266 CA375852682	124	P>L		No	ClinGen gnomAD
rs1445190478 CA375852676	125	P>L		No	ClinGen TOPMed
CA5383608 rs753609650	127	E>*		No	ClinGen ExAC gnomAD
CA5383607 rs766204078	129	N>S		No	ClinGen ExAC gnomAD
rs1361735443 CA375852625	133	R>G		No	ClinGen gnomAD
rs1225770732 CA375852579	139	Q>H		No	ClinGen TOPMed
rs750432879 CA5383605	139	Q>P		No	ClinGen ExAC TOPMed gnomAD
rs750432879 CA5383604	139	Q>R		No	ClinGen ExAC TOPMed gnomAD
rs1456970203 CA375852577	140	S>T		No	ClinGen gnomAD
CA375852560 rs373164047	142	G>D		No	ClinGen ESP ExAC TOPMed gnomAD
CA5383602 rs373164047	142	G>V		No	ClinGen ESP ExAC TOPMed gnomAD
rs1275100909 CA375852556	143	I>V		No	ClinGen TOPMed
CA201212648 rs112339683	146	E>G		No	ClinGen Ensembl
rs1294796559 CA375852527	147	H>Y		No	ClinGen gnomAD
rs1456417561 CA375852511	149	I>L		No	ClinGen TOPMed
rs1010235978 CA201212647	150	D>A		No	ClinGen TOPMed
CA5383596 rs775990387	151	Y>H		No	ClinGen ExAC gnomAD
CA5383595 rs770336567	152	I>V		No	ClinGen ExAC gnomAD
rs1589047998 CA375852438	159	V>A		No	ClinGen Ensembl
rs1253109007 CA375852441	159	V>L		No	ClinGen gnomAD
CA375852427 rs1471048160	161	L>W		No	ClinGen TOPMed
CA201212646 rs878862785	162	N>T		No	ClinGen gnomAD
rs1179836482 CA375852398	165	P>L		No	ClinGen TOPMed
CA375852393 rs781726694	166	N>I		No	ClinGen ExAC TOPMed gnomAD
rs781726694 CA5383593	166	N>S	Variant assessed as Somatic; 0.0 impact. [NCI-TCGA]	No	ClinGen ExAC NCI-TCGA TOPMed gnomAD
rs1424019792 CA375852387	167	E>A		No	ClinGen TOPMed
rs1227161155 CA375852382	168	I>F		No	ClinGen gnomAD
rs1303406137 CA375852355	171	Y>C		No	ClinGen gnomAD
rs747703603 CA5383591	173	Y>*		No	ClinGen ExAC TOPMed
CA5383592 rs770879533	173	Y>C		No	ClinGen ExAC gnomAD
CA5383589 rs777883073	175	S>L		No	ClinGen ExAC gnomAD
CA5383588 rs758589290	176	K>E		No	ClinGen ExAC gnomAD
CA5383587 rs748436217	177	E>K		No	ClinGen ExAC TOPMed gnomAD
rs1168367942 TCGA novel CA375852309	178	E>*	Variant assessed as Somatic; impact. [NCI-TCGA]	No	ClinGen NCI-TCGA gnomAD
rs1168367942 CA375852311	178	E>K		No	ClinGen gnomAD
rs1589047884 CA375852302	179	L>V		No	ClinGen Ensembl
CA375852297 rs1481303857	180	K>E		No	ClinGen gnomAD
CA375852294 rs1589047863	180	K>R		No	ClinGen Ensembl
rs1464601975 CA375852289	181	E>Q		No	ClinGen TOPMed
CA375852282 rs1589047840	182	L>I		No	ClinGen Ensembl
rs779812108 CA5383586	183	L>P		No	ClinGen ExAC gnomAD
CA375852273 rs779812108	183	L>R		No	ClinGen ExAC gnomAD
CA5383584 rs137970796	185	K>T		No	ClinGen 1000Genomes ESP ExAC TOPMed gnomAD
CA375852256 rs1252900140	186	A>P		No	ClinGen gnomAD
rs376567303 CA201212645	187	A>P		No	ClinGen ESP
CA375852227 rs1444895920	190	E>A		No	ClinGen TOPMed
CA201212644 rs147099136	194	T>K		No	ClinGen ESP TOPMed
rs147099136 CA201212643	194	T>M	Variant assessed as Somatic; impact. [NCI-TCGA]	No	ClinGen ESP NCI-TCGA TOPMed
rs768373716 CA201212641	196	W>C		No	ClinGen Ensembl
CA5383583 rs373254659	202	A>P		No	ClinGen ESP ExAC gnomAD
rs767511572 CA5383582	206	F>L		No	ClinGen ExAC TOPMed gnomAD
rs908548897 CA201212639	207	K>*		No	ClinGen TOPMed gnomAD
rs1218030852 CA375852111	207	K>N		No	ClinGen TOPMed
CA5383581 rs757189207	208	W>*		No	ClinGen ExAC gnomAD
rs55998315 CA201212638	209	W>R		No	ClinGen Ensembl
rs1166758900 CA375852060	214	H>N		No	ClinGen TOPMed gnomAD
CA201212637 rs982771346	215	L>V		No	ClinGen TOPMed gnomAD
CA375852036 rs1329254628	217	Q>R		No	ClinGen gnomAD
rs763761173 CA5383579	219	V>G		No	ClinGen ExAC gnomAD
rs1406689747 CA375852007	221	H>R		No	ClinGen gnomAD
rs1378407988 CA375852009	221	H>Y		No	ClinGen TOPMed gnomAD
rs1476909600 CA375851999	222	E>A		No	ClinGen gnomAD
COSM3806413 rs929229161 CA201212636	222	E>K	Variant assessed as Somatic; 0.0 impact. breast [NCI-TCGA, Cosmic]	No	ClinGen cosmic curated NCI-TCGA TOPMed gnomAD
rs1201363945 CA468164539	225	Y>*		No	ClinGen TOPMed gnomAD
CA375851980 rs1477210496 COSM378923	225	Y>H	lung [Cosmic]	No	ClinGen cosmic curated TOPMed
rs1439175262 CA375851965	227	M>V		No	ClinGen gnomAD

No associated diseases with Q13907

1 regional properties for Q13907

Type	Name	Position	InterPro Accession
domain	NUDIX hydrolase domain	49 - 199	IPR000086

Functions

		Description
EC Number	5.3.3.2	Transposing C=C bonds
Subcellular Localization	Peroxisome
PANTHER Family
PANTHER Subfamily
PANTHER Protein Class
PANTHER Pathway Category	No pathway information available

3 GO annotations of cellular component

Name	Definition
cytoplasm	The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
peroxisome	A small organelle enclosed by a single membrane, and found in most eukaryotic cells. Contains peroxidases and other enzymes involved in a variety of metabolic processes including free radical detoxification, lipid catabolism and biosynthesis, and hydrogen peroxide metabolism.

4 GO annotations of molecular function

Name	Definition
isopentenyl-diphosphate delta-isomerase activity	Catalysis of the reaction: isopentenyl diphosphate = dimethylallyl diphosphate.
magnesium ion binding	Binding to a magnesium (Mg) ion.
manganese ion binding	Binding to a manganese ion (Mn).
metal ion binding	Binding to a metal ion.

4 GO annotations of biological process

Name	Definition
cholesterol biosynthetic process	The chemical reactions and pathways resulting in the formation of cholesterol, cholest-5-en-3 beta-ol, the principal sterol of vertebrates and the precursor of many steroids, including bile acids and steroid hormones.
dimethylallyl diphosphate biosynthetic process	The chemical reactions and pathways resulting in the formation of dimethylallyl diphosphate.
isopentenyl diphosphate biosynthetic process	The chemical reactions and pathways resulting in the formation of isopentenyl diphosphate, an isomer of dimethylallyl diphosphate and the key precursor of all isoprenoids.
isoprenoid biosynthetic process	The chemical reactions and pathways resulting in the formation of an isoprenoid compound, isoprene (2-methylbuta-1,3-diene) or compounds containing or derived from linked isoprene (3-methyl-2-butenylene) residues.

1 homologous proteins in AiPD

UniProt AC	Gene Name	Protein Name	Species	Evidence Code
P15496	IDI1	Isopentenyl-diphosphate delta-isomerase	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	PR

10	20	30	40	50	60
MPEINTNHLD	KQQVQLLAEM	CILIDENDNK	IGAETKKNCH	LNENIEKGLL	HRAFSVFLFN
70	80	90	100	110	120
TENKLLLQQR	SDAKITFPGC	FTNTCCSHPL	SNPAELEESD	ALGVRRAAQR	RLKAELGIPL
130	140	150	160	170	180
EEVPPEEINY	LTRIHYKAQS	DGIWGEHEID	YILLVRKNVT	LNPDPNEIKS	YCYVSKEELK
190	200	210	220
ELLKKAASGE	IKITPWFKII	AATFLFKWWD	NLNHLNQFVD	HEKIYRM